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Distefano M, Lanzarotti E, Fernández MF, Mangano A, Martí M, Aulicino P. Identification of novel molecular determinants of co-receptor usage in HIV-1 subtype F V3 envelope sequences. Sci Rep 2020; 10:12583. [PMID: 32724045 PMCID: PMC7387458 DOI: 10.1038/s41598-020-69408-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/30/2020] [Indexed: 02/05/2023] Open
Abstract
HIV-1 determinants of coreceptor usage within the gp120 V3 loop have been broadly studied over the past years. This information has led to the development of state-of the-art bioinformatic tools that are useful to predict co-receptor usage based on the V3 loop sequence mainly of subtypes B, C and A. However, these methods show a poor performance for subtype F V3 loops, which are found in an increasing number of HIV-1 strains worldwide. In the present work we investigated determinants of viral tropisms in the understudied subtype F by looking at genotypic and structural information of coreceptor:V3 loop interactions in a novel group of 40 subtype F V3 loops obtained from HIV-1 strains phenotypically characterized either as syncytium inducing or non-syncytium inducing by the MT-2 assay. We provide novel information about estimated interactions energies between a set of V3 loops with known tropism in subtype F, that allowed us to improve predictions of the coreceptor usage for this subtype. Understanding genetic and structural features underlying HIV coreceptor usage across different subtypes is relevant for the rational design of preventive and therapeutic strategies aimed at limiting the HIV-1 epidemic worldwide.
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Affiliation(s)
- Maximiliano Distefano
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Departamento de Computación, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Fernández
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Aulicino
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina.
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Critical amino acid residues and potential N-linked glycosylation sites contribute to circulating recombinant form 01_AE pathogenesis in Northeast China. AIDS 2019; 33:1431-1439. [PMID: 30889014 PMCID: PMC6635051 DOI: 10.1097/qad.0000000000002197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Supplemental Digital Content is available in the text Objective: The current study aimed to understand epidemiological feature and critical factors associated with pathogenesis of circulating recombinant form (CRF) 01_AE strains in Northeast China. Design: Compared analysis was made between CRF01_AE and non-CRF01_AE samples to understand the pathogenicity features of CRF01_AE. Further analyses between CRF01_AE samples with high or low CD4+ cell counts and between samples with different coreceptor usages were done to explore the possible factors correlating to the pathogenesis of CRF01_AE viruses. Methods: The genotypes of newly identified strains were determined by phylogenetic analyses using Mega 6.06. Coreceptor usage was predicted by Geno2Pheno algorithm. Potential N-linked glycosylation site (PNGS) number was calculated using the online N-glycosite software. The properties of amino acid sequences were analyzed by the online ProtParam tool. Results: CRF01_AE become the main HIV-1 genotype since 2010. Compared with non-CRF01_AE group, the CRF01_AE group showed a higher proportion of samples with CD4+ cell count less than 200 cells/μl. Shorter amino acid length, fewer PNGSs and the presence of a basic motif R/KNXT or NR/KT in V4 correlated to a lower CD4+ cell count, and existence or coexistence of Thr12, Arg13, Val21 and Lys33, presence of more than 4 of net charges and lack of the PNGS within V3 favored to the X4/R5X4 coreceptor usage of CRF01_AE viruses. Conclusion: CRF01_AE has dominated HIV-1 genotype in Northeast China. Infection with CRF01_AE exhibited a fast disease progression, which may be associated with specific amino acid residues and PNGSs in V3 and V4 regions as well as amino acid length of V4 region.
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Hongjaisee S, Nantasenamat C, Carraway TS, Shoombuatong W. HIVCoR: A sequence-based tool for predicting HIV-1 CRF01_AE coreceptor usage. Comput Biol Chem 2019; 80:419-432. [PMID: 31146118 DOI: 10.1016/j.compbiolchem.2019.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/09/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Determination of HIV-1 coreceptor usage is strongly recommended before starting the coreceptor-specific inhibitors for HIV treatment. Currently, the genotypic assays are the most interesting tools due to they are more feasible than phenotypic assays. However, most of prediction models were developed and validated by data set of HIV-1 subtype B and C. The present study aims to develop a powerful and reliable model to accurately predict HIV-1 coreceptor usage for CRF01_AE subtype called HIVCoR. HIVCoR utilized random forest and support vector machine as the prediction model, together with amino acid compositions, pseudo amino acid compositions and relative synonymous codon usage frequencies as the input feature. The overall success rate of 93.79% was achieved from the external validation test on the objective benchmark dataset. Comparison results indicated that HIVCoR was superior to other bioinformatics tools and genotypic predictors. For the convenience of experimental scientists, a user-friendly webserver has been established at http://codes.bio/hivcor/.
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Affiliation(s)
- Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiangmai 50200, Thailand; Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai 50200, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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Alteri C, Scutari R, Bertoli A, Armenia D, Gori C, Fabbri G, Mastroianni CM, Cerva C, Cristaudo A, Vicenti I, Bruzzone B, Zazzi M, Andreoni M, Antinori A, Svicher V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Integrase strand transfer inhibitor-based regimen is related with a limited HIV-1 V3 loop evolution in clinical practice. Virus Genes 2019; 55:290-297. [PMID: 30796743 DOI: 10.1007/s11262-019-01649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Integrase-strand-transfer inhibitors (INSTIs) are known to rapidly reduce HIV-1 plasma viral load, replication cycles, and new viral integrations, thus potentially limiting viral evolution. Here, we assessed the role of INSTIs on HIV-1 V3 evolution in a cohort of 89 HIV-1-infected individuals starting an INSTI- (N = 41, [dolutegravir: N = 1; elvitegravir: N = 3; raltegravir: N = 37]) or a non-INSTI-based (N = 48) combined antiretroviral therapy (cART), with two plasma RNA V3 genotypic tests available (one before [baseline] and one during cART). V3 sequences were analysed for genetic distance (Tajima-Nei model) and positive selection (dN/dS ratio). Individuals were mainly infected by B subtype (71.9%). Median (interquartile-range, IQR) plasma viral load and CD4 + T cell count at baseline were 4.8 (3.5-5.5) log10 copies/mL and 207 (67-441) cells/mm3, respectively. Genetic distance (median, IQR) between the V3 sequences obtained during cART and those obtained at baseline was 0.04 (0.01-0.07). By considering treatment, genetic distance was significantly lower in INSTI-treated than in non-INSTI-treated individuals (median [IQR]: 0.03[0.01-0.04] vs. 0.05[0.02-0.08], p = 0.026). In line with this, a positive selection (defined as dN/dS ≥ 1) was observed in 36.6% of V3 sequences belonging to the INSTI-treated group and in 56.3% of non-INSTI group (p = 0.05). Multivariable logistic regression confirmed the independent correlation of INSTI-based regimens with a lower probability of both V3 evolution (adjusted odds-ratio: 0.35 [confidence interval (CI) 0.13-0.88], p = 0.027) and positive selection (even if with a trend) (adjusted odds-ratio: 0.46 [CI 0.19-1.11], p = 0.083). Overall, this study suggests a role of INSTI-based regimen in limiting HIV-1 V3 evolution over time. Further studies are required to confirm these findings.
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Affiliation(s)
- Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy. .,Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italia.
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,UniCamillus, Saint Camillus International University of Health Sciences, Via di Sant'Alessandro, 8, 00131, Rome, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Gabriele Fabbri
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | | | - Carlotta Cerva
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", Viale Oxford 81, 00133, Rome, Italy
| | - Antonio Cristaudo
- Infectious Dermatology and Allergology Unit, San Gallicano Dermatological Institute, IFO-IRCCS, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnology, University of Siena, Viale Bracci 2, 53100, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, IRCCS AOU San Martino - IST, Largo R. Benzi 10, 16132, Genoa, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Viale Bracci 2, 53100, Siena, Italy
| | - Massimo Andreoni
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", Viale Oxford 81, 00133, Rome, Italy
| | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | | | - Carlo Federico Perno
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italia.,National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
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5
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Alteri C, Fabeni L, Scutari R, Berno G, Di Carlo D, Gori C, Bertoli A, Vergori A, Mastrorosa I, Bellagamba R, Mussini C, Colafigli M, Montella F, Pennica A, Mastroianni CM, Girardi E, Andreoni M, Antinori A, Svicher V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Genetic divergence of HIV-1 B subtype in Italy over the years 2003-2016 and impact on CTL escape prevalence. Sci Rep 2018; 8:15739. [PMID: 30356083 PMCID: PMC6200748 DOI: 10.1038/s41598-018-34058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/04/2018] [Indexed: 12/05/2022] Open
Abstract
HIV-1 is characterized by high genetic variability, with implications for spread, and immune-escape selection. Here, the genetic modification of HIV-1 B subtype over time was evaluated on 3,328 pol and 1,152 V3 sequences belonging to B subtype and collected from individuals diagnosed in Italy between 2003 and 2016. Sequences were analyzed for genetic-distance from consensus-B (Tajima-Nei), non-synonymous and synonymous rates (dN and dS), CTL escapes, and intra-host evolution over four time-spans (2003–2006, 2007–2009, 2010–2012, 2013–2016). Genetic-distance increased over time for both pol and V3 sequences (P < 0.0001 and 0.0003). Similar results were obtained for dN and dS. Entropy-value significantly increased at 16 pol and two V3 amino acid positions. Seven of them were CTL escape positions (protease: 71; reverse-transcriptase: 35, 162, 177, 202, 207, 211). Sequences with ≥3 CTL escapes increased from 36.1% in 2003–2006 to 54.0% in 2013–2016 (P < 0.0001), and showed better intra-host adaptation than those containing ≤2 CTL escapes (intra-host evolution: 3.0 × 10−3 [2.9 × 10−3–3.1 × 10−3] vs. 4.3 × 10−3 [4.0 × 10−3–5.0 × 10−3], P[LRT] < 0.0001[21.09]). These data provide evidence of still ongoing modifications, involving CTL escape mutations, in circulating HIV-1 B subtype in Italy. These modifications might affect the process of HIV-1 adaptation to the host, as suggested by the slow intra-host evolution characterizing viruses with a high number of CTL escapes.
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Affiliation(s)
- Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy.
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Giulia Berno
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20133, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Alessandra Vergori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Ilaria Mastrorosa
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Rita Bellagamba
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | | | | | | | | | | | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | | | - Carlo Federico Perno
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy.,Department of Oncology, University of Milan, Milan, 20122, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
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6
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Bowder D, Hollingsead H, Durst K, Hu D, Wei W, Wiggins J, Medjahed H, Finzi A, Sodroski J, Xiang SH. Contribution of the gp120 V3 loop to envelope glycoprotein trimer stability in primate immunodeficiency viruses. Virology 2018; 521:158-168. [PMID: 29936340 PMCID: PMC6053598 DOI: 10.1016/j.virol.2018.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
Abstract
The V3 loop of the human immunodeficiency virus type 1 (HIV-1) gp120 exterior envelope glycoprotein (Env) becomes exposed after CD4 binding and contacts the coreceptor to mediate viral entry. Prior to CD4 engagement, a hydrophobic patch located at the tip of the V3 loop stabilizes the non-covalent association of gp120 with the Env trimer of HIV-1 subtype B strains. Here, we show that this conserved hydrophobic patch (amino acid residues 307, 309 and 317) contributes to gp120-trimer association in HIV-1 subtype C, HIV-2 and SIV. Changes that reduced the hydrophobicity of these V3 residues resulted in increased gp120 shedding and decreased Env-mediated cell-cell fusion and virus entry in the different primate immunodeficiency viruses tested. Thus, the hydrophobic patch is an evolutionarily conserved element in the tip of the gp120 V3 loop that plays an essential role in maintaining the stability of the pre-triggered Env trimer in diverse primate immunodeficiency viruses. The V3-loop of HIV-1 gp120 contributes to Env trimer stability and viral entry. The hydrophobic patch in the tip of the V3 loop is critical for pre-triggered Env trimer stability. The hydrophobic patch is a conserved motif in primate immunodeficiency viruses.
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Affiliation(s)
- Dane Bowder
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Haley Hollingsead
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Kate Durst
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Duoyi Hu
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Wenzhong Wei
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Joshua Wiggins
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Halima Medjahed
- Centre de Recherche du CHUM, Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, United States; Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02215, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
| | - Shi-Hua Xiang
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
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Hongjaisee S, Braibant M, Barin F, Ngo-Giang-Huong N, Sirirungsi W, Samleerat T. Effect of Amino Acid Substitutions Within the V3 Region of HIV-1 CRF01_AE on Interaction with CCR5-Coreceptor. AIDS Res Hum Retroviruses 2017; 33:946-951. [PMID: 28497977 DOI: 10.1089/aid.2017.0044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Specific amino acids within the V3 loop of HIV-1 CRF01_AE envelope glycoprotein that are involved in the interaction with CCR5/CXCR4 coreceptors, are not well characterized. We generated V3 mutants using polymerase chain reaction (PCR)-based site-directed mutagenesis of HIV-1 CRF01_AE R5-env plasmids at specific positions. Mutant viruses were produced by env-pseudotyped virus assay, tested for coreceptor usage using U373.R5 and U373.X4 cells, and viral entry was assessed with luciferase activity measurement. All viruses, harboring either single or double mutations, used the CCR5 coreceptor. However, those containing a single substitution at positions 7, 11, 18, and 32 and those with mutations at positions 5/32 and 18/32 had reduced infectivity. Only virus with arginine substitution at position 11 seemed to be involved in CXCR4 coreceptor usage. Our results suggest that some V3 positions may be necessary for the binding to coreceptor, but not for the switch of coreceptor usage.
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Affiliation(s)
- Sayamon Hongjaisee
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai, Thailand
| | | | - Francis Barin
- Inserm U966, Université François Rabelais, Tours, France
| | - Nicole Ngo-Giang-Huong
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai, Thailand
- Institut de Recherche pour le Développement (IRD), UMI 174-PHPT, Chiangmai, Thailand
| | - Wasna Sirirungsi
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai, Thailand
| | - Tanawan Samleerat
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai, Thailand
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Dimonte S. Different HIV-1 env frames: gp120 and ASP (antisense protein) biosynthesis, and theirs co-variation tropic amino acid signatures in X4- and R5-viruses. J Med Virol 2016; 89:112-122. [PMID: 27328810 DOI: 10.1002/jmv.24611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 11/07/2022]
Abstract
Antisense protein (ASP) is the new actor of viral life of Human Immunodeficiency Virus type 1 (HIV-1) although proposed above 20 years ago. The asp ORF is into complementary strand of the gp120/gp41 junction of env gene. The ASP biological role remains little known. Knowing the Env markers of viral tropism, a dataset of sequences (660 strains) was used to analyze the hypothetical ASP involvement in CCR5 (R5) and/or CXCR4 (X4) co-receptor interaction. Preliminarily, prevalence of ASP and gp120V3 mutations was performed; following association among mutations were elaborate. The classical V3 tropic-signatures were confirmed, and 36 R5- and 22 X4-tropic ASP mutations were found. Moreover, by analyzing the ASP sequences, 36 out of 179 amino acid positions significantly associated with different co-receptor usage were found. Several statistically significant associations between gp120V3 and ASP mutations were observed. The dendrogram showed the existence of a cluster associated with R5-usage and a large cluster associated with X4-usage. These results show that gp120V3 and specific amino acid changes in ASP are associated together with CXCR4 and/or CCR5-usage. These findings implement previous observations on unclear ASP functions. J. Med. Virol. 89:112-122, 2017. © 2016 Wiley Periodicals, Inc.
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Recent Transmission Clustering of HIV-1 C and CRF17_BF Strains Characterized by NNRTI-Related Mutations among Newly Diagnosed Men in Central Italy. PLoS One 2015; 10:e0135325. [PMID: 26270824 PMCID: PMC4535860 DOI: 10.1371/journal.pone.0135325] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Increased evidence of relevant HIV-1 epidemic transmission in European countries is being reported, with an increased circulation of non-B-subtypes. Here, we present two recent HIV-1 non-B transmission clusters characterized by NNRTI-related amino-acidic mutations among newly diagnosed HIV-1 infected men, living in Rome (Central-Italy). METHODS Pol and V3 sequences were available at the time of diagnosis for all individuals. Maximum-Likelihood and Bayesian phylogenetic-trees with bootstrap and Bayesian-probability supports defined transmission-clusters. HIV-1 drug-resistance and V3-tropism were also evaluated. RESULTS Among 534 new HIV-1 non-B cases, diagnosed from 2011 to 2014, in Central-Italy, 35 carried virus gathering in two distinct clusters, including 27 HIV-1 C and 8 CRF17_BF subtypes, respectively. Both clusters were centralized in Rome, and their origin was estimated to have been after 2007. All individuals within both clusters were males and 37.1% of them had been recently-infected. While C-cluster was entirely composed by Italian men-who-have-sex-with-men, with a median-age of 34 years (IQR:30-39), individuals in CRF17_BF-cluster were older, with a median-age of 51 years (IQR:48-59) and almost all reported sexual-contacts with men and women. All carried R5-tropic viruses, with evidence of atypical or resistance amino-acidic mutations related to NNRTI-drugs (K103Q in C-cluster, and K101E+E138K in CRF17_BF-cluster). CONCLUSIONS These two epidemiological clusters provided evidence of a strong and recent circulation of C and CRF17_BF strains in central Italy, characterized by NNRTI-related mutations among men engaging in high-risk behaviours. These findings underline the role of molecular epidemiology in identifying groups at increased risk of HIV-1 transmission, and in enhancing additional prevention efforts.
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10
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Alteri C, Surdo M, Bellocchi MC, Saccomandi P, Continenza F, Armenia D, Parrotta L, Carioti L, Costa G, Fourati S, Di Santo F, Scutari R, Barbaliscia S, Fedele V, Carta S, Balestra E, Alcaro S, Marcelin AG, Calvez V, Ceccherini-Silberstein F, Artese A, Perno CF, Svicher V. Incomplete APOBEC3G/F Neutralization by HIV-1 Vif Mutants Facilitates the Genetic Evolution from CCR5 to CXCR4 Usage. Antimicrob Agents Chemother 2015; 59:4870-81. [PMID: 26055363 PMCID: PMC4505216 DOI: 10.1128/aac.00137-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
Incomplete APOBEC3G/F neutralization by a defective HIV-1Vif protein can promote genetic diversification by inducing G-to-A mutations in the HIV-1 genome. The HIV-1 Env V3 loop, critical for coreceptor usage, contains several putative APOBEC3G/F target sites. Here, we determined if APOBEC3G/F, in the presence of Vif-defective HIV-1 virus, can induce G-to-A mutations at V3 positions critical to modulation of CXCR4 usage. Peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages (MDM) from 2 HIV-1-negative donors were infected with CCR5-using 81.A-VifWT virus (i.e., with wild-type [WT] Vif protein), 81.A-VifE45G, or 81.A-VifK22E (known to incompletely/partially neutralize APOBEC3G/F). The rate of G-toA mutations was zero or extremely low in 81.A-VifWT- and 81.A-VifE45G-infected PBMC from both donors. Conversely, G-to-A enrichment was detected in 81.A-VifK22E-infected PBMC (prevalence ranging from 2.18% at 7 days postinfection [dpi] to 3.07% at 21 dpi in donor 1 and from 10.49% at 7 dpi to 8.69% at 21 dpi in donor 2). A similar scenario was found in MDM. G-to-A mutations occurred at 8 V3 positions, resulting in nonsynonymous amino acid substitutions. Of them, G24E and E25K strongly correlated with phenotypically/genotypically defined CXCR4-using viruses (P = 0.04 and 5.5e-7, respectively) and increased the CXCR4 N-terminal binding affinity for V3 (WT, -40.1 kcal/mol; G24E, -510 kcal/mol; E25K, -522 kcal/mol). The analysis of paired V3 and Vif DNA sequences from 84 HIV-1-infected patients showed that the presence of a Vif-defective virus correlated with CXCR4 usage in proviral DNA (P = 0.04). In conclusion, incomplete APOBEC3G/F neutralization by a single Vif amino acid substitution seeds a CXCR4-using proviral reservoir. This can have implications for the success of CCR5 antagonist-based therapy, as well as for the risk of disease progression.
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Affiliation(s)
- Claudia Alteri
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Matteo Surdo
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | | | - Patrizia Saccomandi
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | | | - Daniele Armenia
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Lucia Parrotta
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | - Luca Carioti
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Giosuè Costa
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | - Slim Fourati
- Department of Virology, Hospital "Pitie Salpietrere," Paris, France
| | - Fabiola Di Santo
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Rossana Scutari
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Silvia Barbaliscia
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | | | | | - Emanuela Balestra
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Stefano Alcaro
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | | | - Vincent Calvez
- Department of Virology, Hospital "Pitie Salpietrere," Paris, France
| | | | - Anna Artese
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | - Carlo Federico Perno
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy INMI L. Spallanzani, Rome, Italy
| | - Valentina Svicher
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
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Genotypic Tropism Testing in HIV-1 Proviral DNA Can Provide Useful Information at Low-Level Viremia. J Clin Microbiol 2015; 53:2935-41. [PMID: 26135872 DOI: 10.1128/jcm.00893-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/25/2015] [Indexed: 01/24/2023] Open
Abstract
The possibility of performing genotypic tropism testing (GTT) with proviral DNA (pvDNA) even during suppressed viremia would facilitate the use of CCR5 inhibitors as part of switching, simplification, or intensification strategies. Thus, we aimed to evaluate the tropism concordance between plasma RNA and pvDNA samples and to assess which factors could affect possible discrepancies between the two compartments. GTT was performed using both plasma RNA and pvDNA from 55 sample pairs from drug-experienced patients. Potential differences between the two compartments were evaluated by analyzing coreceptor usage and genetic variability. Paired samples were also stratified in three levels of viremia (<50, 51 to 500, and >500 copies/ml). Overall, Geno2Pheno comparisons of false-positive rates in the two compartments showed good correlation (r = 0.72). A high level of concordance in tropism predictions for the two compartments was found (46/55 sample pairs [83.6%]). Among the 9 sample pairs with discordant tropisms, a larger proportion of pvDNA samples harboring CXCR4/dual-mixed-tropic viruses was found, in comparison with plasma RNA samples (88.9% versus 11.1%; P = 0.0034). Discordant samples were characterized by greater genetic variability than were concordant samples. With stratification of the paired samples according to viremia levels, the prevalence of discordant samples decreased with increasing viremia (<50 copies/ml, 21.4%; 51 to 500 copies/ml, 15.4%; >500 copies/ml, 6.7%; P = 0.2). Our findings confirm that prediction of viral tropism using pvDNA is feasible even in low-level viremia and provides useful information for therapy optimization for patients with low or suppressed viremia.
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Kozyryev I, Zhang J. Bayesian analysis of complex interacting mutations in HIV drug resistance and cross-resistance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 827:367-83. [PMID: 25387976 DOI: 10.1007/978-94-017-9245-5_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A successful treatment of AIDS world-wide is severely hindered by the HIV virus' drug resistance capability resulting from complicated mutation patterns of viral proteins. Such a system of mutations enables the virus to survive and reproduce despite the presence of various antiretroviral drugs by disrupting their binding capability. Although these interacting mutation patterns are extremely difficult to efficiently uncover and interpret, they contribute valuable information to personalized therapeutic regimen design. The use of Bayesian statistical modeling provides an unprecedented opportunity in the field of anti-HIV therapy to understand detailed interaction structures of drug resistant mutations. Multiple Bayesian models equipped with Markov Chain Monte Carlo (MCMC) methods have been recently proposed in this field (Zhang et al. in PNAS 107:1321, 2010 [1]; Zhang et al. in J Proteome Sci Comput Biol 1:2, 2012 [2]; Svicher et al. in Antiviral Res 93(1):86-93, 2012 [3]; Svicher et al. in Antiviral Therapy 16(7):1035-1045, 2011 [4]; Svicher et al. in Antiviral Ther 16(4):A14-A14, 2011 [5]; Svicher et al. in Antiviral Ther 16(4):A85-A85, 2011 [6]; Alteri et al. in Signature mutations in V3 and bridging sheet domain of HIV-1 gp120 HIV-1 are specifically associated with dual tropism and modulate the interaction with CCR5 N-Terminus, 2011 [7]). Probabilistically modeling mutations in the HIV-1 protease or reverse transcriptase (RT) isolated from drug-treated patients provides a powerful statistical procedure that first detects mutation combinations associated with single or multiple-drug resistance, and then infers detailed dependence structures among the interacting mutations in viral proteins (Zhang et al. in PNAS 107:1321, 2010 [1]; Zhang et al. in J Proteome Sci Comput Biol 1:2, 2012 [2]). Combined with molecular dynamics simulations and free energy calculations, Bayesian analysis predictions help to uncover genetic and structural mechanisms in the HIV treatment resistance. Results obtained with such stochastic methods pave the way not only for optimization of the use for existing HIV drugs, but also for the development of the new more efficient antiretroviral medicines. In this chapter we survey current challenges in the bioinformatics of anti-HIV therapy, and outline how recently emerged Bayesian methods can help with the clinical management of HIV-1 infection. We will provide a rigorous review of the Bayesian variable partition model and the recursive model selection procedure based on probability theory and mathematical data analysis techniques while highlighting real applications in HIV and HBV studies including HIV drug resistance (Zhang et al. in PNAS 107:1321, 2010 [1]), cross-resistance (Zhang et al. in J Proteome Sci Comput Biol 1:2, 2012 [2]), HIV coreceptor usage (Svicher et al. in Antiviral Therapy 16(7):1035-1045, 2011 [4]; Svicher et al. in Antiviral Ther 16(4):A14-A14, 2011 [5]; Alteri et al. in Signature mutations in V3 and bridging sheet domain of HIV-1 gp120 HIV-1 are specifically associated with dual tropism and modulate the interaction with CCR5 N-Terminus, 2011 [7]), and occult HBV infection (Svicher et al. in Antiviral Res 93(1):86-93, 2012 [3]; Svicher et al. in Antiviral Ther 16(4):A85-A85, 2011 [6]).
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Affiliation(s)
- Ivan Kozyryev
- Department of Physics, Harvard University, Cambridge, MA, USA
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13
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Panos G, Watson DC. Effect of HIV-1 subtype and tropism on treatment with chemokine coreceptor entry inhibitors; overview of viral entry inhibition. Crit Rev Microbiol 2014; 41:473-87. [DOI: 10.3109/1040841x.2013.867829] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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State-of-the-art and dissemination of computational tools for drug-design purposes: a survey among Italian academics and industrial institutions. Future Med Chem 2013; 5:907-27. [PMID: 23682568 DOI: 10.4155/fmc.13.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During the first edition of the Computationally Driven Drug Discovery meeting, held in November 2011 at Dompé Pharma (L'Aquila, Italy), a questionnaire regarding the diffusion and the use of computational tools for drug-design purposes in both academia and industry was distributed among all participants. This is a follow-up of a previously reported investigation carried out among a few companies in 2007. The new questionnaire implemented five sections dedicated to: research group identification and classification; 18 different computational techniques; software information; hardware data; and economical business considerations. In this article, together with a detailed history of the different computational methods, a statistical analysis of the survey results that enabled the identification of the prevalent computational techniques adopted in drug-design projects is reported and a profile of the computational medicinal chemist currently working in academia and pharmaceutical companies in Italy is highlighted.
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15
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Díez-Fuertes F, Delgado E, Vega Y, Fernández-García A, Cuevas MT, Pinilla M, García V, Pérez-Álvarez L, Thomson MM. Improvement of HIV-1 coreceptor tropism prediction by employing selected nucleotide positions of the env gene in a Bayesian network classifier. J Antimicrob Chemother 2013; 68:1471-85. [DOI: 10.1093/jac/dkt077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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16
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Xiang SH, Pacheco B, Bowder D, Yuan W, Sodroski J. Characterization of a dual-tropic human immunodeficiency virus (HIV-1) strain derived from the prototypical X4 isolate HXBc2. Virology 2013; 438:5-13. [PMID: 23369572 DOI: 10.1016/j.virol.2013.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/21/2012] [Accepted: 01/02/2013] [Indexed: 11/25/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) coreceptor usage and tropism can be modulated by the V3 loop sequence of the gp120 exterior envelope glycoprotein. For coreceptors, R5 viruses use CCR5, X4 viruses use CXCR4, and dual-tropic (R5X4) viruses use either CCR5 or CXCR4. To understand the requirements for dual tropism, we derived and analyzed a dual-tropic variant of an X4 virus. Changes in the V3 base, which allow gp120 to interact with the tyrosine-sulfated CCR5 N-terminus, and deletion of residues 310/311 in the V3 tip were necessary for efficient CCR5 binding and utilization. Thus, both sets of V3 changes allowed CCR5 utilization with retention of the ability to use CXCR4. We also found that the stable association of gp120 with the trimeric envelope glycoprotein complex in R5X4 viruses, as in X4 viruses, is less sensitive to V3 loop changes than gp120-trimer association in R5 viruses.
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Affiliation(s)
- Shi-hua Xiang
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02215, USA.
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17
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Chen M, Svicher V, Artese A, Costa G, Alteri C, Ortuso F, Parrotta L, Liu Y, Liu C, Perno CF, Alcaro S, Zhang J. Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. ACTA ACUST UNITED AC 2013; 29:451-60. [PMID: 23297034 DOI: 10.1093/bioinformatics/btt002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION To define V3 genetic elements and structural features underlying different HIV-1 co-receptor usage in vivo. RESULTS By probabilistically modeling mutations in the viruses isolated from HIV-1 B subtype patients, we present a unique statistical procedure that would first identify V3 determinants associated with the usage of different co-receptors cooperatively or independently, and then delineate the complicated interactions among mutations functioning cooperatively. We built a model based on dual usage of CXCR4 and CCR5 co-receptors. The molecular basis of our statistical predictions is further confirmed by phenotypic and molecular modeling analyses. Our results provide new insights on molecular basis of different HIV-1 co-receptor usage. This is critical to optimize the use of genotypic tropism testing in clinical practice and to obtain molecular-implication for design of vaccine and new entry-inhibitors.
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Affiliation(s)
- Mengjie Chen
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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18
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Galkin AN, Bychenko AB, Kuznecovs G, Filinova EY. Isolation, characterization, and sequence analysis of a novel HIV type 1 subtype A1 strain from Russia. AIDS Res Hum Retroviruses 2012; 28:1139-46. [PMID: 22236080 DOI: 10.1089/aid.2011.0302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A new syncytia-inducing human immunodeficiency virus type 1 (HIV-1) strain designated PokA79 was first isolated from a peripheral blood mononuclear cells (PBMC) pool from 24 HIV-1-infected patients from Russia and adapted to growth in MT2, MT4, and U937 cell cultures. The full-length genome of this isolate was amplified by RT-two-round PCR and sequenced. The obtained sequence belongs to the A1 subtype and clustered with other A1 former Soviet Union (FSU) strains. Full-length genome analysis showed that some of the PokA79 genes contain insertions and frame shifts, and the gp120 V3 loop has the three amino acid insertion inside its apex, which is rare for subtype A1 sequences. Nonidentical insertions of the same size are also present in the V3 apex region of several HIV-1 sequences from Central Africa.
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Affiliation(s)
- Alexander N. Galkin
- Molecular Genetics Department, Advanced Biomedical Research Laboratory, Moscow, Russia
| | - Andrey B. Bychenko
- Cellular Biology Department, Advanced Biomedical Research Laboratory, Moscow, Russia
| | - Grigorije Kuznecovs
- Physics Analysis Methods Department, Advanced Biomedical Research Laboratory, Moscow, Russia
| | - Elena Y. Filinova
- Cellular Biology Department, Advanced Biomedical Research Laboratory, Moscow, Russia
- in vivo Assays Department, Advanced Biomedical Research Laboratory, Moscow, Russia
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19
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Santoro MM, Armenia D, Fabeni L, Santoro M, Gori C, Forbici F, Svicher V, Bertoli A, Dori L, Surdo M, Balestra E, Palamara G, Girardi E, Angarano G, Andreoni M, Narciso P, Antinori A, Ceccherini-Silberstein F, Perno CF. The lowest X4 Geno2Pheno false-positive rate is associated with greater CD4 depletion in HIV-1 infected patients. Clin Microbiol Infect 2012; 18:E289-98. [PMID: 22681969 DOI: 10.1111/j.1469-0691.2012.03905.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Through this study we evaluated whether the HIV-1 tropism determined by genotypic analysis correlates with HIV-1 markers, such as CD4 cell count and plasma HIV-RNA. The analysis was performed on 1221 HIV-1 B-subtype infected patients with an available V3 sequence (all maraviroc naive). Of them, 532 were antiretroviral therapy (ART) naive and 689 ART experienced. Tropism determination was performed by using the geno2pheno (co-receptor) algorithm set at a false-positive rate (FPR) of 10% and 2%. Potential associations of FPR with CD4 cell count and viraemia were evaluated. Association of V3 mutations with genotypic-determined tropism was also evaluated according to different FPR ranges. About 26% of patients (either ART naive or ART experienced) were infected by X4-tropic viruses (using the classical 10% FPR cut-off). However, a significantly lower proportion of ART-naive patients had FPR ≤ 2% in comparison with ART-experienced patients (4.9% vs. 12.6%, respectively, p <0.001). The risk of advanced HIV-1 infection (with CD4 cell count ≤ 200 cells/mm(3)) was significantly greater in X4-infected patients, either ART-naive (OR (95% CI)), 4.2 (1.8-9.2); p 0.0006) or ART-experienced (2.3 (1.4-3.6); p 0.0003), with FPR set at 2% (but not at 10%). This finding was confirmed by multivariable logistic analysis. No relationship was found between viraemia and FPR ≤2%. Some X4-related mutations were significantly associated with FPR ≤2% (ART-naive patients, S11R, Y21V, G24K and G24R, p ≤0.001; ART-experienced patients, Y7K, S11R, H13Y, p ≤0.002). In conclusion, these findings show that within the context of genotypically-assessed CXCR4 tropism, FPR ≤2% defines (far better than 10%-FPR) a viral population associated with low CD4 rank, with potentially greater cytopathic effect, and with more advanced disease.
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